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spades
|
public |
SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies.
|
2024-12-13 |
|
virulign
|
public |
VIRULIGN is a tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins.
|
2024-12-13 |
|
nedbit-features-calculator
|
public |
Network diffusion and biology-informed topological features
|
2024-12-13 |
|
macs2
|
public |
Model Based Analysis for ChIP-Seq data
|
2024-12-13 |
|
prinseq-plus-plus
|
public |
PRINSEQ++ - Multi-threaded C++ sequence cleaning
|
2024-12-13 |
|
ucsc-bigbedsummary
|
public |
Extract summary information from a bigBed file.
|
2024-12-13 |
|
ucsc-pslscore
|
public |
calculate web blat score from psl files
|
2024-12-13 |
|
ncbi-ngs-sdk
|
public |
NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
|
2024-12-13 |
|
abundancebin
|
public |
No Summary
|
2024-12-13 |
|
xtandem
|
public |
No Summary
|
2024-12-13 |
|
yahs
|
public |
YaHS, yet another Hi-C scaffolding tool.
|
2024-12-13 |
|
fasta3
|
public |
The FASTA package - protein and DNA sequence similarity searching and alignment programs
|
2024-12-13 |
|
slamem
|
public |
slamem bioconda package from https://github.com/fjdf/slaMEM
|
2024-12-13 |
|
minimap
|
public |
Experimental tool to find approximate mapping positions between long sequences
|
2024-12-13 |
|
genomethreader
|
public |
GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments.
|
2024-12-13 |
|
libdivsufsort
|
public |
No Summary
|
2024-12-13 |
|
2pg_cartesian
|
public |
2pg cartesian is a framework of optimization algorithms for protein structure prediction.
|
2024-12-13 |
|
naf
|
public |
Compressed binary file format for DNA/RNA/protein sequence data
|
2024-12-13 |
|
r-mmcpcounter
|
public |
Murine version of MCP-counter, a tool to estimate the immune and stromal composition of heterogeneous tissue, from transcriptomic data
|
2024-12-13 |
|
r-r0
|
public |
Estimation of R0 and Real-Time Reproduction Number from Epidemics.
|
2024-12-13 |
|
revoluzer
|
public |
Genome rearrangement analysis tools
|
2024-12-13 |
|
pretextsnapshot
|
public |
Commandline image generator for Pretext Hi-C genome contact maps.
|
2024-12-13 |
|
ucsc-paranodestart
|
public |
version 12.18
|
2024-12-13 |
|
karect
|
public |
Read error correction tool based on multiple alignment.
|
2024-12-13 |
|
allegro
|
public |
A fast linkage and haplotype analysis utility making use of MTBDD to reduce complexity.
|
2024-12-13 |
|
unimap
|
public |
Unimap is a fork of minimap2 optimized for assembly-to-reference alignment.
|
2024-12-13 |
|
gwama
|
public |
Genome-Wide Association Meta Analysis
|
2024-12-13 |
|
fwdpy11
|
public |
Forward-time population genetic simulation in Python.
|
2024-12-13 |
|
psass
|
public |
Comparison of pooled-sequencing data for two populations
|
2024-12-13 |
|
pandora
|
public |
Pan-genome inference and genotyping with long noisy or short accurate reads
|
2024-12-13 |
|
veryfasttree
|
public |
VeryFastTree -- speeding up the estimation of phylogenies for large alignments through parallelization and vectorization strategies.
|
2024-12-13 |
|
r-presto
|
public |
Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment.
|
2024-12-13 |
|
digestiflow-cli
|
public |
Command line client for Digestiflow.
|
2024-12-13 |
|
gxf2chrom
|
public |
Everything in .chrom from GTF/GFF
|
2024-12-13 |
|
lrge
|
public |
Genome size estimation from long read overlaps
|
2024-12-13 |
|
usalign
|
public |
Universal structure alignment of monomeric, complex proteins and nucleic acids
|
2024-12-13 |
|
rgccacmd
|
public |
Multiblock data analysis concerns the analysis of several sets of variables (blocks) observed on the same group of individuals. The main aims of the RGCCA package are (i) to study the relationships between blocks and (ii) to identify subsets of variables of each block which are active in their relationships with the other blocks.
|
2024-12-13 |
|
pgma-simple
|
public |
No Summary
|
2024-12-13 |
|
r-lymphclon
|
public |
We provide a clonality score estimator that takes full advantage of the multi-biological-replicate structure of modern sequencing experiments; it specifically takes into account the reality that, typically, the clonal coverage is well below 0.1%.
|
2024-12-13 |
|
ucsc-bedweedoverlapping
|
public |
Filter out beds that overlap a 'weed.bed' file.
|
2024-12-13 |
|
meryl
|
public |
No Summary
|
2024-12-13 |
|
mmannot
|
public |
mmannot annotates reads, or quantifies the features. mmmannot takes special care of multi-mapping reads.
|
2024-12-13 |
|
pretextgraph
|
public |
Embeds bedgraph data into Pretext contact maps.
|
2024-12-13 |
|
ska
|
public |
SKA (Split Kmer Analysis)
|
2024-12-13 |
|
coils
|
public |
A generalized profile syntax for biomolecular sequence motifs and its function in automatic sequence interpretation.
|
2024-12-13 |
|
ucsc-dbsnoop
|
public |
Produce an overview of a database.
|
2024-12-13 |
|
fmlrc
|
public |
A long-read error correction tool using the multi-string Burrows Wheeler Transform
|
2024-12-13 |
|
estscan
|
public |
No Summary
|
2024-12-13 |
|
get_orfs
|
public |
Fast extraction of ORFs in all possible translation tables
|
2024-12-13 |
|
ucsc-linestora
|
public |
generate .ra format from lines with pipe-separated fields
|
2024-12-13 |
